diff --git a/src/simplefold/cli.py b/src/simplefold/cli.py
index 99230fa..2068424 100644
--- a/src/simplefold/cli.py
+++ b/src/simplefold/cli.py
@@ -27,6 +27,7 @@ def main():
     parser.add_argument("--plddt", action="store_true", help="Enable pLDDT prediction.")
     parser.add_argument("--output_format", type=str, default="mmcif", choices=["pdb", "mmcif"], help="Output file format.")
     parser.add_argument("--backend", type=str, default='torch', choices=['torch', 'mlx'], help="Backend to run inference either torch or mlx")
+    parser.add_argument("--cache", type=str, default=None, help="Specify the cache directory other than default.")
     parser.add_argument("--seed", type=int, default=42, help="Random seed for reproducibility.")
     parser.add_argument(
         "--version",
diff --git a/src/simplefold/inference.py b/src/simplefold/inference.py
index 3221b85..7b6533f 100644
--- a/src/simplefold/inference.py
+++ b/src/simplefold/inference.py
@@ -62,7 +62,7 @@ def initialize_folding_model(args):
     if not os.path.exists(ckpt_path):
         os.makedirs(ckpt_dir, exist_ok=True)
         os.system(f"curl -L {ckpt_url_dict[simplefold_model]} -o {ckpt_path}")
-    cfg_path = os.path.join("configs/model/architecture", f"foldingdit_{simplefold_model[11:]}.yaml")
+    cfg_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture", f"foldingdit_{simplefold_model[11:]}.yaml")
 
     checkpoint = torch.load(ckpt_path, map_location="cpu", weights_only=False)
 
@@ -100,7 +100,7 @@ def initialize_plddt_module(args, device):
         os.makedirs(args.ckpt_dir, exist_ok=True)
         os.system(f"curl -L {plddt_ckpt_url} -o {plddt_ckpt_path}")
 
-    plddt_module_path = "configs/model/architecture/plddt_module.yaml"
+    plddt_module_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture/plddt_module.yaml")
     plddt_checkpoint = torch.load(plddt_ckpt_path, map_location="cpu", weights_only=False)
 
     if args.backend == "torch":
@@ -128,7 +128,7 @@ def initialize_plddt_module(args, device):
         os.makedirs(args.ckpt_dir, exist_ok=True)
         os.system(f"curl -L {ckpt_url_dict['simplefold_1.6B']} -o {plddt_latent_ckpt_path}")
 
-    plddt_latent_config_path = "configs/model/architecture/foldingdit_1.6B.yaml"
+    plddt_latent_config_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture/foldingdit_1.6B.yaml")
     plddt_latent_checkpoint = torch.load(plddt_latent_ckpt_path, map_location="cpu", weights_only=False)
 
     if args.backend == "torch":
@@ -257,7 +257,7 @@ def predict_structures_from_fastas(args):
     output_dir.mkdir(parents=True, exist_ok=True)
     prediction_dir = output_dir / f"predictions_{args.simplefold_model}"
     prediction_dir.mkdir(parents=True, exist_ok=True)
-    cache = output_dir / "cache"
+    cache = output_dir / "cache" if not args.cache else Path(args.cache)
     cache.mkdir(parents=True, exist_ok=True)
 
     # set random seed for reproducibility
diff --git a/src/simplefold/wrapper.py b/src/simplefold/wrapper.py
index add3734..0481258 100644
--- a/src/simplefold/wrapper.py
+++ b/src/simplefold/wrapper.py
@@ -88,6 +88,7 @@ def from_pretrained_folding_model(self):
 
         # load model checkpoint
         cfg_path = os.path.join(
+            Path(__file__).parents[2], 
             "configs/model/architecture", f"foldingdit_{simplefold_model[11:]}.yaml"
         )
         if self.backend == "torch":
@@ -126,7 +127,7 @@ def from_pretrained_plddt_model(self):
         if not os.path.exists(plddt_ckpt_path):
             os.system(f"curl -L -o {plddt_ckpt_path} {plddt_ckpt_url}")
 
-        plddt_module_path = "configs/model/architecture/plddt_module.yaml"
+        plddt_module_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture/plddt_module.yaml")
         plddt_checkpoint = torch.load(
             plddt_ckpt_path, map_location="cpu", weights_only=False
         )
@@ -162,7 +163,7 @@ def from_pretrained_plddt_model(self):
                 f"curl -L -o {plddt_latent_ckpt_path} {ckpt_url_dict['simplefold_1.6B']}"
             )
 
-        plddt_latent_config_path = "configs/model/architecture/foldingdit_1.6B.yaml"
+        plddt_latent_config_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture/foldingdit_1.6B.yaml")
         plddt_latent_checkpoint = torch.load(
             plddt_latent_ckpt_path, map_location="cpu", weights_only=False
         )